Related papers: Understanding Reaction Mechanisms from Start to Fi…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
We present a methodology for training foundational transformer models capable of processing collider data with diverse kinematic signatures. Our universal foundation model is designed for simultaneous analysis of all processes involving…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
We perform a systematic study of capture excitation functions by using an empirical coupled-channel model. In this model, a barrier distribution is used to take effectively into account the effects of couplings between the relative motion…
A chain of interacting spin behaves like a quantum mediator (quantum link) which allows two distant parties that control the ends of the chain to exchange quantum messages. We show that over repeated uses without resetting the study of a…
Swarming patterns that emerge from the interaction of many mobile agents are a subject of great interest in fields ranging from biology to physics and robotics. In some application areas, multiple swarms effectively interact and collide,…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…
Even when starting with a very poor initial guess, the iterative configuration interaction (iCI) approach can converge from above to full CI very quickly by constructing and diagonalizing a small Hamiltonian matrix at each…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
Contour integrals in the complex plane are the basis of effective numerical methods for computing matrix functions, such as the matrix exponential and the Mittag-Leffler function. These methods provide successful ways to solve partial…
Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has…
We propose a control design method for linear time-invariant systems that iteratively learns to satisfy unknown polyhedral state constraints. At each iteration of a repetitive task, the method constructs an estimate of the unknown…
We describe a simple method to compute the Cramer-Rao limit of a high energy experiment, i.e., the smallest error with which a parameter can in principle be determined in a reaction. This precision remains a theoretical paradigm since it…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
The critical point of the condensation transition for linear molecules adsorbed on square lattices, was studied by using an adaptation of the Histogram Reweighting technique. The results were obtained by means of grand canonical Monte Carlo…